2026-01-25 23:11
ftp://ftp.de.debian.org/debian/pool/main/s/stringtie/stringtie_3.0.3+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.8.0-90-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.69
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0
cppcheck: head 2.19.0
head-info: 73b2ad6 (2026-01-25 10:16:47 +0100)
count: 1876 1822
elapsed-time: 71.4 71.0
head-timing-info:

old-timing-info:

head results:
gpertea-stringtie-4b2320a/bundle.h:156:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/bundle.h:164:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/bundle.h:212:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/bundle.h:293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/bundle.cpp:157:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable txCmpByExons [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/bundle.cpp:191:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::nascent_only' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::rcount' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::ucount' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::mrcount' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::movlcount' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::avg' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::stdev' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::mavg' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/tablemaker.h:51:2: warning:inconclusive: Member variable 'RC_Feature::mstdev' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning:inconclusive: Member variable 'CReadAln::segs' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning: Member variable 'CReadAln::aligned_polyT' is not initialized in the copy constructor. [uninitMemberVar]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning: Member variable 'CReadAln::aligned_polyA' is not initialized in the copy constructor. [uninitMemberVar]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning: Member variable 'CReadAln::unaligned_polyT' is not initialized in the copy constructor. [uninitMemberVar]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning: Member variable 'CReadAln::unaligned_polyA' is not initialized in the copy constructor. [uninitMemberVar]
gpertea-stringtie-4b2320a/bundle.h:198:2: warning:inconclusive: Member variable 'CReadAln::sort_tiebreaker' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
gpertea-stringtie-4b2320a/bundle.h:205:3: performance: Variable 'pair_count' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
gpertea-stringtie-4b2320a/bundle.h:206:3: performance: Variable 'pair_idx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
gpertea-stringtie-4b2320a/bundle.h:207:3: performance: Variable 'juncs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
gpertea-stringtie-4b2320a/tablemaker.h:41:8: style:inconclusive: Technically the member function 'RC_Feature::PCompare::operator()' can be const. [functionConst]
gpertea-stringtie-4b2320a/tablemaker.h:193:8: style:inconclusive: Technically the member function 'RC_MultiCovInc::operator()' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:68:8: style:inconclusive: Technically the member function 'GRefData::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:71:8: style:inconclusive: Technically the member function 'GRefData::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:99:7: style:inconclusive: Technically the member function 'GPtFeature::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:100:7: style:inconclusive: Technically the member function 'GPtFeature::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:118:8: style:inconclusive: Technically the member function 'GRefPtData::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:121:8: style:inconclusive: Technically the member function 'GRefPtData::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:155:7: style:inconclusive: Either there is a missing 'override', or the member function 'CJunction::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/bundle.h:163:7: style:inconclusive: Either there is a missing 'override', or the member function 'CJunction::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/tablemaker.h:244:4: warning: Struct 'RC_BundleData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:244:4: warning: Struct 'RC_BundleData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/tablemaker.h:46:2: style: Struct 'RC_Feature' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:121:2: style: Struct 'RC_ExonOvl' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:155:2: style: Struct 'RC_TData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:190:2: style: Class 'RC_MultiCovInc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:228:2: style: Struct 'RC_BundleData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:44:3: style: Struct 'GRefData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:97:2: style: Struct 'GPtFeature' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:109:3: style: Struct 'GRefPtData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:136:2: style: Struct 'TAlnInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:152:2: style: Struct 'CJunction' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:194:2: style: Struct 'CReadAln' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:243:2: style: Struct 'GReadAlnData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:266:2: style: Struct 'CBundle' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/bundle.h:284:9: style: Struct 'CPrediction' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/tablemaker.h:265:18: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/bundle.h:22:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/bundle.cpp:55:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/bundle.cpp:10:42: style:inconclusive: Function 'getGuideStatus' argument 1 names different: declaration 't' definition 'guide'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:33:42: note: Function 'getGuideStatus' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:10:42: note: Function 'getGuideStatus' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:13:29: style:inconclusive: Function 'setGuideStatus' argument 1 names different: declaration 't' definition 'guide'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:34:29: note: Function 'setGuideStatus' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:13:29: note: Function 'setGuideStatus' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:23:25: style:inconclusive: Function 'setNascent' argument 1 names different: declaration 't' definition 'guide'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:12:25: note: Function 'setNascent' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:23:25: note: Function 'setNascent' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:23:37: style:inconclusive: Function 'setNascent' argument 2 names different: declaration 'v' definition 'nasc_st'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:12:33: note: Function 'setNascent' argument 2 names different: declaration 'v' definition 'nasc_st'.
gpertea-stringtie-4b2320a/bundle.cpp:23:37: note: Function 'setNascent' argument 2 names different: declaration 'v' definition 'nasc_st'.
gpertea-stringtie-4b2320a/bundle.cpp:32:24: style:inconclusive: Function 'isNascent' argument 1 names different: declaration 't' definition 'guide'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:14:24: note: Function 'isNascent' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:32:24: note: Function 'isNascent' argument 1 names different: declaration 't' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:45:36: style:inconclusive: Function 'keepGuide' argument 1 names different: declaration 'scaff' definition 'guide'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:371:25: note: Function 'keepGuide' argument 1 names different: declaration 'scaff' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:45:36: note: Function 'keepGuide' argument 1 names different: declaration 'scaff' definition 'guide'.
gpertea-stringtie-4b2320a/bundle.cpp:45:56: style:inconclusive: Function 'keepGuide' argument 2 names different: declaration 'ref_rc_data' definition 'ref_rc'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:371:45: note: Function 'keepGuide' argument 2 names different: declaration 'ref_rc_data' definition 'ref_rc'.
gpertea-stringtie-4b2320a/bundle.cpp:45:56: note: Function 'keepGuide' argument 2 names different: declaration 'ref_rc_data' definition 'ref_rc'.
gpertea-stringtie-4b2320a/bundle.cpp:172:59: style:inconclusive: Function 'evalReadAln' argument 2 names different: declaration 'strand' definition 'xstrand'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/bundle.h:393:48: note: Function 'evalReadAln' argument 2 names different: declaration 'strand' definition 'xstrand'.
gpertea-stringtie-4b2320a/bundle.cpp:172:59: note: Function 'evalReadAln' argument 2 names different: declaration 'strand' definition 'xstrand'.
gpertea-stringtie-4b2320a/bundle.h:216:7: style: Local variable 'len' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/bundle.h:174:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/bundle.h:216:7: note: Shadow variable
gpertea-stringtie-4b2320a/bundle.cpp:105:20: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/bundle.cpp:71:14: note: Shadowed declaration
gpertea-stringtie-4b2320a/bundle.cpp:105:20: note: Shadow variable
gpertea-stringtie-4b2320a/bundle.cpp:124:22: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/bundle.cpp:71:14: note: Shadowed declaration
gpertea-stringtie-4b2320a/bundle.cpp:124:22: note: Shadow variable
gpertea-stringtie-4b2320a/bundle.h:68:29: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:71:28: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:118:31: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:121:30: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:155:28: style: Parameter 'b' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:163:29: style: Parameter 'b' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/bundle.h:364:23: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:292:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.h:528:16: warning:inconclusive: Member variable 'GDynArray < char * >::byptr' is not assigned a value in 'GDynArray < char * >::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GBase.h:528:16: warning:inconclusive: Member variable 'GDynArray < char >::byptr' is not assigned a value in 'GDynArray < char >::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:12: style: Unused private function: 'GArgs::validOpt' [unusedPrivateFunction]
gpertea-stringtie-4b2320a/gclib/GArgs.h:57:8: note: Unused private function: 'GArgs::validOpt'
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:12: note: Unused private function: 'GArgs::validOpt'
gpertea-stringtie-4b2320a/gclib/GBase.h:386:8: style:inconclusive: Technically the member function 'GSeg::len' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:387:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:391:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:395:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:399:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:403:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:409:7: style:inconclusive: Technically the member function 'GSeg::overlapLen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:420:7: style:inconclusive: Technically the member function 'GSeg::overlapLen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:435:8: style:inconclusive: Technically the member function 'GSeg::contains' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:438:8: style:inconclusive: Technically the member function 'GSeg::contained' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:442:8: style:inconclusive: Technically the member function 'GSeg::equals' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:445:8: style:inconclusive: Technically the member function 'GSeg::equals' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:450:8: style:inconclusive: Technically the member function 'GSeg::coordMatch' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:466:8: style:inconclusive: Technically the member function 'GSeg::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:469:8: style:inconclusive: Technically the member function 'GSeg::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:685:8: style:inconclusive: Technically the member function 'GLineReader::readcount' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:689:8: style:inconclusive: Technically the member function 'GLineReader::tlength' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:690:8: style:inconclusive: Technically the member function 'GLineReader::linelen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:692:9: style:inconclusive: Technically the member function 'GLineReader::isEof' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:693:9: style:inconclusive: Technically the member function 'GLineReader::eof' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:694:10: style:inconclusive: Technically the member function 'GLineReader::getfpos' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:695:10: style:inconclusive: Technically the member function 'GLineReader::getFpos' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:12: style:inconclusive: Technically the member function 'GArgs::validOpt' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:57:8: note: Technically the member function 'GArgs::validOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:12: note: Technically the member function 'GArgs::validOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:289:12: style:inconclusive: Technically the member function 'GArgs::validShortOpt' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:58:8: note: Technically the member function 'GArgs::validShortOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:289:12: note: Technically the member function 'GArgs::validShortOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:295:12: style:inconclusive: Technically the member function 'GArgs::validLongOpt' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:59:8: note: Technically the member function 'GArgs::validLongOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:295:12: note: Technically the member function 'GArgs::validLongOpt' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:314:12: style:inconclusive: Technically the member function 'GArgs::isError' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:72:8: note: Technically the member function 'GArgs::isError' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:314:12: note: Technically the member function 'GArgs::isError' can be const.
gpertea-stringtie-4b2320a/gclib/GArgs.h:73:8: style:inconclusive: Technically the member function 'GArgs::getCount' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:74:8: style:inconclusive: Technically the member function 'GArgs::getFmtCount' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GArgs.h:75:8: style:inconclusive: Technically the member function 'GArgs::getNonOptCount' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:579:10: style:inconclusive: Technically the member function 'GDynArray < char * >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:580:10: style:inconclusive: Technically the member function 'GDynArray < char * >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:579:10: style:inconclusive: Technically the member function 'GDynArray < char >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:580:10: style:inconclusive: Technically the member function 'GDynArray < char >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:718:28: warning: Class 'GLineReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:718:28: warning: Class 'GLineReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/GBase.h:381:3: style: Struct 'GSeg' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:478:2: style: Struct 'GRangeParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:706:4: style: Class 'GLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:713:4: style: Class 'GLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:512:5: style: Class 'GDynArray < char * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:512:5: style: Class 'GDynArray < char >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:84:44: style: Redundant condition: The condition '_argv[p][1] == 0' is redundant since '_argv[p][1] != '-'' is sufficient. [redundantCondition]
gpertea-stringtie-4b2320a/gclib/GBase.h:253:6: warning: Possible null pointer dereference: ptr [nullPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:291:9: note: Assignment 'tmp=NULL', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:292:15: note: Calling function 'GMalloc', 1st argument '(voidpointer*)tmp' value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:253:6: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GBase.h:254:19: warning: Possible null pointer dereference: ptr [nullPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:291:9: note: Assignment 'tmp=NULL', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:292:15: note: Calling function 'GMalloc', 1st argument '(voidpointer*)tmp' value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:254:19: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GBase.h:255:13: warning: Possible null pointer dereference: ptr [nullPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:291:9: note: Assignment 'tmp=NULL', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:292:15: note: Calling function 'GMalloc', 1st argument '(voidpointer*)tmp' value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:255:13: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GBase.h:292:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:294:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:294:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:482:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:28:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:42:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:53:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:91:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:95:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:107:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:108:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:112:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:167:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:198:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:212:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:266:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:280:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:281:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:283:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:284:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:286:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:299:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:303:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:514:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:519:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:526:42: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:584:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:612:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:619:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:638:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:25: style:inconclusive: Function 'validOpt' argument 1 names different: declaration 'c' definition 'code'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GArgs.h:57:21: note: Function 'validOpt' argument 1 names different: declaration 'c' definition 'code'.
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:307:25: note: Function 'validOpt' argument 1 names different: declaration 'c' definition 'code'.
gpertea-stringtie-4b2320a/gclib/GBase.h:595:32: performance: Function parameter 'arr' should be passed by const reference. [passedByValue]
gpertea-stringtie-4b2320a/gclib/GBase.h:391:22: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GBase.h:395:22: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GBase.h:442:21: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GBase.h:466:25: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GBase.h:469:24: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:295:31: style: Parameter 'o' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:295:40: style: Parameter 'to' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:387:22: style: Parameter 'd' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:409:24: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:435:23: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:438:24: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:445:21: style: Parameter 'd' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:450:25: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GArgs.cpp:77:8: style: Variable 'f' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:22:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:45:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:70:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:146:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:194:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:246:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:255:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:520:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:549:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:954:25: style: Condition 'endptr==start' is always false [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:21:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:80:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:87:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:96:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:205:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:229:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:235:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:390:25: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:393:46: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:465:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:472:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:474:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:484:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:484:33: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:487:19: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:489:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:583:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:590:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:600:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:637:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:654:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:656:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:750:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:1015:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:735:8: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:762:7: style: The scope of the variable 'g' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:515:34: style:inconclusive: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GBase.h:727:34: note: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'.
gpertea-stringtie-4b2320a/gclib/GBase.cpp:515:34: note: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'.
gpertea-stringtie-4b2320a/gclib/GBase.cpp:144:9: style: Variable 'cdir' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:250:38: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:453:50: style: Parameter 'to' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:471:36: style: Parameter 'newvalue' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:480:26: style: Parameter 'part' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:654:9: style: Variable 'smax' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:904:8: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:908:8: style: Variable 'atdigits' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:927:9: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:930:9: style: Variable 'atdigits' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:945:8: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:963:8: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GBase.cpp:227:17: style: Variable 'mkdir_err' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:19:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:33:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:48:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:103:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable used [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:132:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:141:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable used [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:136:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:382:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:408:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:417:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:160:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:176:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:239:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:254:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:276:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:292:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:345:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:355:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:362:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:395:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:401:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:410:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:450:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:506:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:521:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:546:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:573:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:623:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:650:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:664:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:83:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:395:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable freeItems [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:422:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable freeItems [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:449:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable freeItems [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable used [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:271:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable used [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:281:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:332:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:346:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:360:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:373:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:283:35: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1454:54: style:inconclusive: Boolean expression 'len>=16' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:80:17: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Add' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:88:17: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:97:14: style: Either there is a missing 'override', or the member function 'GHashSet::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:111:14: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:115:14: style: Either there is a missing 'override', or the member function 'GHashSet::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:119:6: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:141:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:165:21: style:inconclusive: Either there is a missing 'override', or the member function 'GStrSet::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:213:10: style:inconclusive: Technically the member function 'GPVec::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:214:10: style:inconclusive: Technically the member function 'GPVec::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:215:9: style:inconclusive: Technically the member function 'GPVec::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:216:9: style:inconclusive: Technically the member function 'GPVec::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: style:inconclusive: Technically the member function 'GPVec::IndexOf' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:229:9: note: Technically the member function 'GPVec::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: note: Technically the member function 'GPVec::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GList.hh:64:10: style:inconclusive: Technically the member function 'GArray::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:66:10: style:inconclusive: Technically the member function 'GArray::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:109:10: style:inconclusive: Technically the member function 'GList::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:132:9: style:inconclusive: Technically the member function 'GList::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:28:8: style:inconclusive: Technically the member function 'GFastaRec::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:31:8: style:inconclusive: Technically the member function 'GFastaRec::operator>' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:34:8: style:inconclusive: Technically the member function 'GFastaRec::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:52:8: style:inconclusive: Technically the member function 'GFastaIndex::hasIndex' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:134:7: style:inconclusive: Technically the member function 'GFaSeqGet::getsublen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:135:7: style:inconclusive: Technically the member function 'GFaSeqGet::getseqlen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:136:9: style:inconclusive: Technically the member function 'GFaSeqGet::getseqofs' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:137:7: style:inconclusive: Technically the member function 'GFaSeqGet::getLineLen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:138:7: style:inconclusive: Technically the member function 'GFaSeqGet::getLineBLen' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:412:21: style:inconclusive: Either there is a missing 'override', or the member function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:45:3: warning: Class 'GFaSeqGet' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:45:3: warning: Class 'GFaSeqGet' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:303:13: warning: Class 'GFastaDb' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:303:13: warning: Class 'GFastaDb' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GFastaRec * > , KHashMapHash < KHashMapBucket < const char * , GFastaRec * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GFastaRec * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GFastaRec * > , KHashMapHash < KHashMapBucket < const char * , GFastaRec * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GFastaRec * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , GFastaRec * > , KHashMapHash < KHashMapBucket < const char * , GFastaRec * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GFastaRec * > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , GFastaRec * > , KHashMapHash < KHashMapBucket < const char * , GFastaRec * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GFastaRec * > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GFastaRec * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:179:14: warning: The class 'GStrSet' defines member function with name 'Clear' also defined in its parent class 'GHashSet'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:97:14: note: Parent function 'GHashSet::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:179:14: note: Derived function 'GStrSet::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:190:14: warning: The class 'GStrSet' defines member function with name 'Reset' also defined in its parent class 'GHashSet'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:101:14: note: Parent function 'GHashSet::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:190:14: note: Derived function 'GStrSet::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Add' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: warning: The class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Reset' also defined in its parent class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:269:14: note: Parent function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: note: Derived function 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GList.hh:228:39: warning: The class 'GArray' defines member function with name 'Add' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:369:37: note: Parent function 'GVec::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:228:39: note: Derived function 'GArray::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:51:9: warning: The class 'GArray' defines member function with name 'Add' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:59:9: note: Parent function 'GVec::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:51:9: note: Derived function 'GArray::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:56:9: warning: The class 'GArray' defines member function with name 'cAdd' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:60:9: note: Parent function 'GVec::cAdd'
gpertea-stringtie-4b2320a/gclib/GList.hh:56:9: note: Derived function 'GArray::cAdd'
gpertea-stringtie-4b2320a/gclib/GList.hh:57:9: warning: The class 'GArray' defines member function with name 'cPush' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:65:9: note: Parent function 'GVec::cPush'
gpertea-stringtie-4b2320a/gclib/GList.hh:57:9: note: Derived function 'GArray::cPush'
gpertea-stringtie-4b2320a/gclib/GList.hh:58:9: warning: The class 'GArray' defines member function with name 'Push' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:64:9: note: Parent function 'GVec::Push'
gpertea-stringtie-4b2320a/gclib/GList.hh:58:9: note: Derived function 'GArray::Push'
gpertea-stringtie-4b2320a/gclib/GList.hh:360:40: warning: The class 'GArray' defines member function with name 'Sort' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:541:38: note: Parent function 'GVec::Sort'
gpertea-stringtie-4b2320a/gclib/GList.hh:360:40: note: Derived function 'GArray::Sort'
gpertea-stringtie-4b2320a/gclib/GList.hh:353:40: warning: The class 'GArray' defines member function with name 'Replace' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:451:38: note: Parent function 'GVec::Replace'
gpertea-stringtie-4b2320a/gclib/GList.hh:353:40: note: Derived function 'GArray::Replace'
gpertea-stringtie-4b2320a/gclib/GList.hh:336:40: warning: The class 'GArray' defines member function with name 'Insert' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:420:38: note: Parent function 'GVec::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:336:40: note: Derived function 'GArray::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:76:10: warning: The class 'GArray' defines member function with name 'Insert' also defined in its parent class 'GVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:51:10: note: Parent function 'GVec::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:76:10: note: Derived function 'GArray::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:495:38: warning: The class 'GList' defines member function with name 'Add' also defined in its parent class 'GPVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:783:38: note: Parent function 'GPVec::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:495:38: note: Derived function 'GList::Add'
gpertea-stringtie-4b2320a/gclib/GList.hh:662:39: warning: The class 'GList' defines member function with name 'Sort' also defined in its parent class 'GPVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:932:39: note: Parent function 'GPVec::Sort'
gpertea-stringtie-4b2320a/gclib/GList.hh:662:39: note: Derived function 'GList::Sort'
gpertea-stringtie-4b2320a/gclib/GList.hh:636:39: warning: The class 'GList' defines member function with name 'Insert' also defined in its parent class 'GPVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:793:39: note: Parent function 'GPVec::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:636:39: note: Derived function 'GList::Insert'
gpertea-stringtie-4b2320a/gclib/GList.hh:642:39: warning: The class 'GList' defines member function with name 'Move' also defined in its parent class 'GPVec'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GVec.hh:806:39: note: Parent function 'GPVec::Move'
gpertea-stringtie-4b2320a/gclib/GList.hh:642:39: note: Derived function 'GList::Move'
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:180:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:181:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:184:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:32:5: style: Class 'GArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:33:5: style: Class 'GArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:98:5: style: Class 'GList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:102:5: style: Class 'GList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:21:3: style: Class 'GFastaRec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:58:3: style: Class 'GFastaIndex' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:67:3: style: Class 'GFaSeqGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:76:3: style: Class 'GFaSeqGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:151:3: style: Class 'GFastaDb' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:394:2: style: Class 'GHash < GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:82:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_used [nullPointerOutOfMemory]
gpertea-stringtie-4b2320a/gclib/khashl.hh:81:36: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/gclib/khashl.hh:81:14: note: Assignment 'new_used=(uint32_t*)std::malloc(__kh_fsize(new_nb)*4)', assigned value is 0
gpertea-stringtie-4b2320a/gclib/khashl.hh:82:10: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/xxhash.h:1172:41: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1172:75: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1400:39: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1403:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1450:27: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1702:41: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1702:75: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1942:39: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1945:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1990:27: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3502:52: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3503:35: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3504:35: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3518:52: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3519:35: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3591:27: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3592:27: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3755:38: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3755:65: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3762:32: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3850:35: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3850:62: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3852:37: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3852:64: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3854:38: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3854:65: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3855:43: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3910:24: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3938:23: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3948:33: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3986:27: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4122:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4219:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4493:38: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4532:52: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4549:56: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4582:36: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4582:63: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4584:38: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4584:65: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4586:39: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4586:66: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4604:34: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4669:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4715:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4716:31: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/wyhash.h:119:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:20:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:34:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:49:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:103:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:103:22: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:172:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:184:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:192:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:192:22: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GVec.hh:28:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GVec.hh:29:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GVec.hh:778:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GVec.hh:875:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:26:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:26:30: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:27:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:27:37: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:87:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:87:30: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:88:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:88:37: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:521:26: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:521:43: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:546:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:546:26: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:74:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:75:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:32:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:80:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:83:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:219:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:227:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:256:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:266:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:290:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:300:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:301:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:13:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:17:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:22:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:23:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:23:30: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:24:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:73:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:259:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:261:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:261:19: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:294:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:295:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:315:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:315:25: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:317:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:325:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:333:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:333:36: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:339:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:348:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:348:39: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:353:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:421:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:436:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:450:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:462:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:470:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:470:22: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:271:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:271:22: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/khashl.hh:81:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/khashl.hh:86:18: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/khashl.hh:110:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1457:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1463:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1519:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1996:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:2002:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:2062:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:3976:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4208:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/xxhash.h:4734:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/khashl.hh:78:16: style: Same expression on both sides of '>'. [duplicateExpression]
gpertea-stringtie-4b2320a/gclib/GVec.hh:555:8: style: Variable 'fCount' is reassigned a value before the old one has been used. [redundantAssignment]
gpertea-stringtie-4b2320a/gclib/GVec.hh:551:8: note: fCount is assigned
gpertea-stringtie-4b2320a/gclib/GVec.hh:555:8: note: fCount is overwritten
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:188:13: style: Redundant initialization for 'newstart'. The initialized value is overwritten before it is read. [redundantInitialization]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:181:16: note: newstart is initialized
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:188:13: note: newstart is overwritten
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:188:5: style: Variable 'newstart' is assigned an expression that holds the same value. [redundantAssignment]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:176:14: note: qstart is assigned 'cstart' here.
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:182:22: note: Assuming condition is false
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:188:5: note: Variable 'newstart' is assigned an expression that holds the same value.
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:217:10: style: Variable 'qlen' is reassigned a value before the old one has been used. [redundantAssignment]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:194:9: note: qlen is assigned
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:217:10: note: qlen is overwritten
gpertea-stringtie-4b2320a/gclib/xxhash.h:3540:19: style: The scope of the variable 'kSecretPtr' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/wyhash.h:221:23: style: The scope of the variable 'h2' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GVec.hh:512:9: style: The scope of the variable 'j' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GVec.hh:897:9: style: The scope of the variable 'J' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GVec.hh:898:7: style: The scope of the variable 'P' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GList.hh:306:8: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GList.hh:586:14: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.cpp:304:8: style: The scope of the variable 'rdone' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/khashl.hh:141:18: style: The scope of the variable 'k' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/xxhash.h:1387:62: style:inconclusive: Function 'XXH_INLINE_XXH32' argument 2 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:297:62: note: Function 'XXH_INLINE_XXH32' argument 2 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1387:62: note: Function 'XXH_INLINE_XXH32' argument 2 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1421:52: style:inconclusive: Function 'XXH_INLINE_XXH32_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:327:52: note: Function 'XXH_INLINE_XXH32_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1421:52: note: Function 'XXH_INLINE_XXH32_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1421:83: style:inconclusive: Function 'XXH_INLINE_XXH32_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:327:84: note: Function 'XXH_INLINE_XXH32_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1421:83: note: Function 'XXH_INLINE_XXH32_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1441:29: style:inconclusive: Function 'XXH_INLINE_XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:330:59: note: Function 'XXH_INLINE_XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1441:29: note: Function 'XXH_INLINE_XXH32_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1441:62: style:inconclusive: Function 'XXH_INLINE_XXH32_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:330:95: note: Function 'XXH_INLINE_XXH32_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1441:62: note: Function 'XXH_INLINE_XXH32_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1504:64: style:inconclusive: Function 'XXH_INLINE_XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:331:65: note: Function 'XXH_INLINE_XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1504:64: note: Function 'XXH_INLINE_XXH32_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1929:62: style:inconclusive: Function 'XXH_INLINE_XXH64' argument 2 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:386:62: note: Function 'XXH_INLINE_XXH64' argument 2 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1929:62: note: Function 'XXH_INLINE_XXH64' argument 2 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1962:52: style:inconclusive: Function 'XXH_INLINE_XXH64_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:392:52: note: Function 'XXH_INLINE_XXH64_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1962:52: note: Function 'XXH_INLINE_XXH64_copyState' argument 1 names different: declaration 'dst_state' definition 'dstState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1962:83: style:inconclusive: Function 'XXH_INLINE_XXH64_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:392:84: note: Function 'XXH_INLINE_XXH64_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1962:83: note: Function 'XXH_INLINE_XXH64_copyState' argument 2 names different: declaration 'src_state' definition 'srcState'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1981:30: style:inconclusive: Function 'XXH_INLINE_XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:395:59: note: Function 'XXH_INLINE_XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1981:30: note: Function 'XXH_INLINE_XXH64_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1981:63: style:inconclusive: Function 'XXH_INLINE_XXH64_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:395:95: note: Function 'XXH_INLINE_XXH64_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:1981:63: note: Function 'XXH_INLINE_XXH64_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:2041:64: style:inconclusive: Function 'XXH_INLINE_XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:396:65: note: Function 'XXH_INLINE_XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:2041:64: note: Function 'XXH_INLINE_XXH64_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3861:53: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:457:53: note: Function 'XXH_INLINE_XXH3_64bits' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3861:53: note: Function 'XXH_INLINE_XXH3_64bits' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3867:36: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits_withSecret' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:482:64: note: Function 'XXH_INLINE_XXH3_64bits_withSecret' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3867:36: note: Function 'XXH_INLINE_XXH3_64bits_withSecret' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3873:34: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits_withSeed' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:466:62: note: Function 'XXH_INLINE_XXH3_64bits_withSeed' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:3873:34: note: Function 'XXH_INLINE_XXH3_64bits_withSeed' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4120:34: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits_update' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:520:64: note: Function 'XXH_INLINE_XXH3_64bits_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4120:34: note: Function 'XXH_INLINE_XXH3_64bits_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4120:67: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:520:100: note: Function 'XXH_INLINE_XXH3_64bits_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4120:67: note: Function 'XXH_INLINE_XXH3_64bits_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4161:69: style:inconclusive: Function 'XXH_INLINE_XXH3_64bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:521:70: note: Function 'XXH_INLINE_XXH3_64bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4161:69: note: Function 'XXH_INLINE_XXH3_64bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4593:55: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:536:55: note: Function 'XXH_INLINE_XXH3_128bits' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4593:55: note: Function 'XXH_INLINE_XXH3_128bits' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4601:37: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits_withSecret' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:538:66: note: Function 'XXH_INLINE_XXH3_128bits_withSecret' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4601:37: note: Function 'XXH_INLINE_XXH3_128bits_withSecret' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4609:35: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits_withSeed' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:537:64: note: Function 'XXH_INLINE_XXH3_128bits_withSeed' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4609:35: note: Function 'XXH_INLINE_XXH3_128bits_withSeed' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4617:20: style:inconclusive: Function 'XXH_INLINE_XXH128' argument 1 names different: declaration 'data' definition 'input'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:725:49: note: Function 'XXH_INLINE_XXH128' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4617:20: note: Function 'XXH_INLINE_XXH128' argument 1 names different: declaration 'data' definition 'input'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4667:35: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits_update' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:557:65: note: Function 'XXH_INLINE_XXH3_128bits_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4667:35: note: Function 'XXH_INLINE_XXH3_128bits_update' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4667:68: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits_update' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:557:101: note: Function 'XXH_INLINE_XXH3_128bits_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4667:68: note: Function 'XXH_INLINE_XXH3_128bits_update' argument 3 names different: declaration 'length' definition 'len'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4673:71: style:inconclusive: Function 'XXH_INLINE_XXH3_128bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/xxhash.h:558:71: note: Function 'XXH_INLINE_XXH3_128bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/xxhash.h:4673:71: note: Function 'XXH_INLINE_XXH3_128bits_digest' argument 1 names different: declaration 'statePtr' definition 'state'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:465:49: style:inconclusive: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:89:21: note: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:465:49: note: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:471:49: style:inconclusive: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:90:21: note: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:471:49: note: Function 'Delete' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:511:48: style:inconclusive: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:41:20: note: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:511:48: note: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:511:55: style:inconclusive: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:41:27: note: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:511:55: note: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'.
gpertea-stringtie-4b2320a/gclib/GList.hh:375:53: style:inconclusive: Function 'GList' argument 1 names different: declaration 'list' definition 'other'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GList.hh:101:24: note: Function 'GList' argument 1 names different: declaration 'list' definition 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:375:53: note: Function 'GList' argument 1 names different: declaration 'list' definition 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:382:52: style:inconclusive: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GList.hh:102:23: note: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GList.hh:382:52: note: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/khashl.hh:93:6: style: Local variable 'key' shadows outer function [shadowFunction]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/khashl.hh:93:6: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/GVec.hh:28:7: style: Variable 'o1' can be declared as reference to const [constVariableReference]
gpertea-stringtie-4b2320a/gclib/GVec.hh:29:7: style: Variable 'o2' can be declared as reference to const [constVariableReference]
gpertea-stringtie-4b2320a/gclib/GVec.hh:344:57: style: Parameter 'item' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GVec.hh:451:60: style: Parameter 'item' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GList.hh:353:62: style: Parameter 'item' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:28:30: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:31:29: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.h:34:29: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:270:20: style: Variable 'farec' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GVec.hh:369:46: style: Parameter 'item' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/wyhash.h:220:127: style: Parameter 'secret' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GList.hh:376:42: warning:inconclusive: Access of moved variable 'other'. [accessMoved]
gpertea-stringtie-4b2320a/gclib/GList.hh:376:15: note: Calling std::move(other)
gpertea-stringtie-4b2320a/gclib/GList.hh:376:42: note: Access of moved variable 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:376:71: warning:inconclusive: Access of moved variable 'other'. [accessMoved]
gpertea-stringtie-4b2320a/gclib/GList.hh:376:15: note: Calling std::move(other)
gpertea-stringtie-4b2320a/gclib/GList.hh:376:71: note: Access of moved variable 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:462:19: warning:inconclusive: Access of moved variable 'list'. [accessMoved]
gpertea-stringtie-4b2320a/gclib/GList.hh:461:28: note: Calling std::move(list)
gpertea-stringtie-4b2320a/gclib/GList.hh:462:19: note: Access of moved variable 'list'.
gpertea-stringtie-4b2320a/gclib/GList.hh:463:14: warning:inconclusive: Access of moved variable 'list'. [accessMoved]
gpertea-stringtie-4b2320a/gclib/GList.hh:461:28: note: Calling std::move(list)
gpertea-stringtie-4b2320a/gclib/GList.hh:463:14: note: Access of moved variable 'list'.
gpertea-stringtie-4b2320a/gclib/wyhash.h:222:12: style: Variable 'h2' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:176:25: style: Variable 'fainamelen' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:250:51: style: Variable 'slen' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:283:41: style: Variable 'doFree' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GVec.hh:551:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:565:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:575:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:591:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:609:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:626:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:634:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:644:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:654:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:663:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:674:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:698:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:709:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:722:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:730:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:735:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:740:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:777:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:786:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:795:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:808:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:822:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:827:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:832:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:841:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:853:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:862:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:874:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:883:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:890:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:903:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:927:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:109:10: style:inconclusive: Either there is a missing 'override', or the member function 'GList < GFastaRec >::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:132:9: style:inconclusive: Either there is a missing 'override', or the member function 'GList < GFastaRec >::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:98:5: style: Class 'GList < GFastaRec >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:102:5: style: Class 'GList < GFastaRec >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:35:20: warning: Either the condition 'fai_name==NULL' is redundant or there is possible null pointer dereference: fai_name. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:32:17: note: Assuming that condition 'fai_name==NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:35:20: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:46:8: warning: Either the condition 'p==NULL' is redundant or there is possible null pointer dereference: p. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:45:12: note: Assuming that condition 'p==NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:46:8: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:71:20: warning: Either the condition 'fa_name==NULL' is redundant or there is possible null pointer dereference: fa_name. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:69:16: note: Assuming that condition 'fa_name==NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:71:20: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:172:25: warning: If resource allocation fails, then there is a possible null pointer dereference: fai [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:149:20: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:149:20: note: Assignment 'fai=fopen(finame,"w")', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:151:27: note: Calling function 'storeIndex', 1st argument 'fai' value is 0
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:172:25: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:179:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fai [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:149:20: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:149:20: note: Assignment 'fai=fopen(finame,"w")', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:151:27: note: Calling function 'storeIndex', 1st argument 'fai' value is 0
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:179:10: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:47:8: warning: Either the condition 'p==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:45:12: note: Assuming that condition 'p==NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:47:8: note: Null pointer addition
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:99:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:140:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:152:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:375:53: style:inconclusive: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'other'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GList.hh:101:24: note: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:375:53: note: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'other'.
gpertea-stringtie-4b2320a/gclib/GList.hh:382:52: style:inconclusive: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GList.hh:102:23: note: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GList.hh:382:52: note: Function 'GList < GFastaRec >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GFastaIndex.cpp:120:23: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GSam.h:309:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:310:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:311:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:317:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREAD1 [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:323:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:327:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:331:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FSECONDARY [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:376:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CRAM_OPT_REFERENCE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.h:533:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:12:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable novel [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:191:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:200:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:344:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:358:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_str [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:377:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GBase.h:528:16: warning:inconclusive: Member variable 'GDynArray < uint32_t >::byptr' is not assigned a value in 'GDynArray < uint32_t >::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GList.hh:64:10: style:inconclusive: Either there is a missing 'override', or the member function 'GArray::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:66:10: style:inconclusive: Either there is a missing 'override', or the member function 'GArray::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:56:9: style:inconclusive: Technically the member function 'GSamRecord::isHardClipped' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:57:9: style:inconclusive: Technically the member function 'GSamRecord::isSoftClipped' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:58:9: style:inconclusive: Technically the member function 'GSamRecord::hasIntrons' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:184:14: style: The member function 'GSamRecord::bam_update' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GSam.h:256:10: style: The member function 'GSamRecord::parse_error' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GSam.h:308:11: style:inconclusive: Technically the member function 'GSamRecord::flags' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:309:7: style:inconclusive: Technically the member function 'GSamRecord::isUnmapped' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:310:7: style:inconclusive: Technically the member function 'GSamRecord::isMapped' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:311:7: style:inconclusive: Technically the member function 'GSamRecord::isPaired' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:314:6: style:inconclusive: Technically the member function 'GSamRecord::pairOrder' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:321:7: style:inconclusive: Technically the member function 'GSamRecord::revStrand' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:326:7: style:inconclusive: Technically the member function 'GSamRecord::alnStrand' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:330:7: style:inconclusive: Technically the member function 'GSamRecord::isPrimary' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:333:14: style:inconclusive: Technically the member function 'GSamRecord::refName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:337:17: style:inconclusive: Technically the member function 'GSamRecord::refId' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:338:17: style:inconclusive: Technically the member function 'GSamRecord::mate_refId' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:339:14: style:inconclusive: Technically the member function 'GSamRecord::mate_refName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:343:17: style:inconclusive: Technically the member function 'GSamRecord::insertSize' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:344:17: style:inconclusive: Technically the member function 'GSamRecord::mate_start' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:345:17: style:inconclusive: Technically the member function 'GSamRecord::mapq' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:399:16: style:inconclusive: Technically the member function 'GSamReader::fileName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:403:16: style:inconclusive: Technically the member function 'GSamReader::refName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < GSeg >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < GSeg >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < GSeg >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < GSeg >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:579:10: style:inconclusive: Technically the member function 'GDynArray < uint32_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBase.h:580:10: style:inconclusive: Technically the member function 'GDynArray < uint32_t >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GSam.h:62:4: style: Class 'GSamRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GSam.h:391:4: style: Class 'GSamReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < GSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBase.h:512:5: style: Class 'GDynArray < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GSam.h:374:12: warning: Either the condition 'hts_file==NULL' is redundant or there is possible null pointer dereference: hts_file. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/GSam.h:372:20: note: Assuming that condition 'hts_file==NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/GSam.h:374:12: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GSam.h:179:23: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.h:239:71: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.h:420:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.h:485:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:51:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:316:43: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:352:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:354:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:365:18: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:367:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:65:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:70:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:83:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:88:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:96:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:100:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:96:15: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:100:15: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:201:12: style: Local variable 'cigar' shadows outer function [shadowFunction]
gpertea-stringtie-4b2320a/gclib/GSam.h:357:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/GSam.cpp:201:12: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/GSam.cpp:201:12: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:365:10: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GSam.h:191:19: style: Variable 'retval' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GSam.h:239:18: style: Variable 'retval' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:137:21: style: Variable 'num_mismatches' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:144:11: style: Variable 'gpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:145:11: style: Variable 'rpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:151:11: style: Variable 'gpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:161:11: style: Variable 'rpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:168:21: style: Variable 'num_mismatches' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:171:11: style: Variable 'rpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:178:21: style: Variable 'num_mismatches' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:179:12: style: Variable 'gpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GSam.cpp:187:11: style: Variable 'gpos' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1403:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1418:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:214:24: warning: Either the condition 'idx<0' is redundant or the array 'my_data->chars[1]' is accessed at index -1, which is out of bounds. [negativeIndex]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:213:11: note: Assuming that condition 'idx<0' is not redundant
gpertea-stringtie-4b2320a/gclib/GStr.cpp:214:24: note: Negative array index
gpertea-stringtie-4b2320a/gclib/GStr.cpp:893:26: warning: Either the condition 'idx<0' is redundant or the array 'data->chars[1]' is accessed at index -1, which is out of bounds. [negativeIndex]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:887:12: note: Assuming that condition 'idx<0' is not redundant
gpertea-stringtie-4b2320a/gclib/GStr.cpp:893:26: note: Negative array index
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1150:45: warning: Either the condition 'start_index<0' is redundant or the array 'my_data->chars[1]' is accessed at index -1, which is out of bounds. [negativeIndex]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1148:21: note: Assuming that condition 'start_index<0' is not redundant
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1150:45: note: Negative array index
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1084:17: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:753:56: warning: Either the condition 'len<0' is redundant or ::memcpy() argument nr 3 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:746:40: note: Assuming that condition 'len<0' is not redundant
gpertea-stringtie-4b2320a/gclib/GStr.cpp:753:56: note: Invalid argument
gpertea-stringtie-4b2320a/gclib/GStr.cpp:217:13: warning: Member variable 'GStr::fTokenDelimiter' is not assigned a value in 'GStr::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:217:13: warning: Member variable 'GStr::fLastTokenStart' is not assigned a value in 'GStr::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:217:13: warning: Member variable 'GStr::fTokenizeMode' is not assigned a value in 'GStr::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:217:13: warning: Member variable 'GStr::readbuf' is not assigned a value in 'GStr::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:217:13: warning: Member variable 'GStr::readbufsize' is not assigned a value in 'GStr::operator='. [operatorEqVarError]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1476:12: style:inconclusive: Technically the member function 'GStr::to' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:79:14: note: Technically the member function 'GStr::to' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1476:12: note: Technically the member function 'GStr::to' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1482:12: style:inconclusive: Technically the member function 'GStr::from' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:81:14: note: Technically the member function 'GStr::from' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1482:12: note: Technically the member function 'GStr::from' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1488:11: style:inconclusive: Technically the member function 'GStr::count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:116:13: note: Technically the member function 'GStr::count' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1488:11: note: Technically the member function 'GStr::count' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1398:11: style:inconclusive: Technically the member function 'GStr::asInt' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:119:13: note: Technically the member function 'GStr::asInt' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1398:11: note: Technically the member function 'GStr::asInt' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1413:14: style:inconclusive: Technically the member function 'GStr::asReal' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:120:16: note: Technically the member function 'GStr::asReal' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1413:14: note: Technically the member function 'GStr::asReal' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1417:12: style:inconclusive: Technically the member function 'GStr::asReal' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:122:14: note: Technically the member function 'GStr::asReal' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1417:12: note: Technically the member function 'GStr::asReal' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1402:12: style:inconclusive: Technically the member function 'GStr::asInt' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GStr.h:124:14: note: Technically the member function 'GStr::asInt' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1402:12: note: Technically the member function 'GStr::asInt' can be const.
gpertea-stringtie-4b2320a/gclib/GStr.h:34:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GStr.h:35:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GStr.h:37:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GStr.h:38:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:21:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:39:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:61:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:64:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:83:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:197:14: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:198:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:199:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:421:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:430:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:438:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:445:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:830:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:833:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:859:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1022:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1043:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1079:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1107:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1197:19: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1197:45: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1261:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1263:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1275:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1283:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1284:29: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1302:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1308:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1316:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1317:29: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1324:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1340:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1344:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1346:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1365:37: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1368:20: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1368:29: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1385:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:762:8: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:825:8: style: The scope of the variable 'dest' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1430:7: style: The scope of the variable 'buf' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1454:7: style: The scope of the variable 'buf' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:202:28: style:inconclusive: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:41:30: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:202:28: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:210:27: style:inconclusive: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:42:29: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:210:27: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:734:23: style:inconclusive: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:78:25: note: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:734:23: note: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:776:29: style:inconclusive: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:114:30: note: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:776:29: note: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:776:48: style:inconclusive: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:114:48: note: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:776:48: note: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:818:34: style:inconclusive: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:94:35: note: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:818:34: note: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:818:53: style:inconclusive: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:94:53: note: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:818:53: note: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:872:22: style:inconclusive: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:86:23: note: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:872:22: note: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:901:39: style:inconclusive: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:92:40: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:901:39: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:931:38: style:inconclusive: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:93:40: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:931:38: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:964:39: style:inconclusive: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:95:41: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:964:39: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:988:39: style:inconclusive: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:96:41: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:988:39: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1067:32: style:inconclusive: Function 'append' argument 1 names different: declaration 'm' definition 's'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GStr.h:100:34: note: Function 'append' argument 1 names different: declaration 'm' definition 's'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1067:32: note: Function 'append' argument 1 names different: declaration 'm' definition 's'.
gpertea-stringtie-4b2320a/gclib/GStr.cpp:787:10: style: Variable 's' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1280:8: style: Variable 'delpos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1315:10: style: Variable 'token_end' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/GStr.cpp:1281:10: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GThreads.h:284:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:149:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:452:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
gpertea-stringtie-4b2320a/gclib/GThreads.h:755:12: style:inconclusive: Technically the member function 'GThread::getStackSize' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GThreads.h:759:31: style:inconclusive: Technically the member function 'GThread::native_handle' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GThreads.h:764:17: style: The member function 'GThread::yield' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GThreads.h:685:3: style: Struct 'GThreadData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GThreads.h:712:5: style: Class 'GThread' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GThreads.h:727:5: style: Class 'GThread' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:362:6: style: The statement 'if (!mNotAThread) mNotAThread=true' is logically equivalent to 'mNotAThread=true'. [duplicateConditionalAssign]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:369:17: note: Assignment 'mNotAThread=true'
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:362:6: note: Condition '!mNotAThread' is redundant
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:210:29: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:252:28: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:271:56: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GThreads.cpp:280:60: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/codons.h:34:14: warning: Either the condition 'idx>2' is redundant or the array 'nuc[3]' is accessed at index 3, which is out of bounds. [arrayIndexOutOfBoundsCond]
gpertea-stringtie-4b2320a/gclib/codons.h:32:20: note: Assuming that condition 'idx>2' is not redundant
gpertea-stringtie-4b2320a/gclib/codons.h:34:14: note: Array index out of bounds
gpertea-stringtie-4b2320a/gclib/codons.h:34:14: warning: Either the condition 'idx<0' is redundant or the array 'nuc[3]' is accessed at index -1, which is out of bounds. [negativeIndex]
gpertea-stringtie-4b2320a/gclib/codons.h:32:11: note: Assuming that condition 'idx<0' is not redundant
gpertea-stringtie-4b2320a/gclib/codons.h:34:14: note: Negative array index
gpertea-stringtie-4b2320a/gclib/codons.h:40:14: warning: Either the condition 'idx>2' is redundant or the array 'nuc[3]' is accessed at index 3, which is out of bounds. [arrayIndexOutOfBoundsCond]
gpertea-stringtie-4b2320a/gclib/codons.h:38:20: note: Assuming that condition 'idx>2' is not redundant
gpertea-stringtie-4b2320a/gclib/codons.h:40:14: note: Array index out of bounds
gpertea-stringtie-4b2320a/gclib/codons.h:40:14: warning: Either the condition 'idx<0' is redundant or the array 'nuc[3]' is accessed at index -1, which is out of bounds. [negativeIndex]
gpertea-stringtie-4b2320a/gclib/codons.h:38:11: note: Assuming that condition 'idx<0' is not redundant
gpertea-stringtie-4b2320a/gclib/codons.h:40:14: note: Negative array index
gpertea-stringtie-4b2320a/gclib/codons.h:11:2: style: Struct 'Codon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/codons.cpp:60:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/codons.cpp:83:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/codons.h:11:14: style: Parameter 'str' can be declared as pointer to const. However it seems that 'Codon' is a callback function, if 'str' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gpertea-stringtie-4b2320a/gclib/codons.h:9:8: note: You might need to cast the function pointer here
gpertea-stringtie-4b2320a/gclib/codons.h:11:14: note: Parameter 'str' can be declared as pointer to const
gpertea-stringtie-4b2320a/gclib/gdna.cpp:56:9: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gdna.cpp:24:22: style: Parameter 'nt' can be declared as pointer to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:195:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:206:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:467:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:696:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1219:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1411:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1492:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1503:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.h:1527:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:254:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dest [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:489:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable skipLine [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1227:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1332:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1434:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gff_warns [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1538:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable transcripts_Only [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1577:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable keep_Attrs [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1605:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gff_warns [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1657:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_BED [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1728:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_BED [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1941:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2127:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable child_idx [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2421:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2858:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:370:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fUnique [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:383:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fUnique [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:394:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:400:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:409:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:437:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:449:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:462:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:471:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:498:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:638:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:643:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GList.hh:663:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:246:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:256:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:268:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:278:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:289:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:302:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:316:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:323:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:328:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:335:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:345:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:371:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:381:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:394:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:404:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:414:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:424:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:452:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:457:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:472:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:485:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:504:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:516:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:537:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/gclib/GVec.hh:136:9: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
gpertea-stringtie-4b2320a/gclib/gff.h:89:5: performance: Variable 'jbits' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
gpertea-stringtie-4b2320a/gclib/GList.hh:109:10: style:inconclusive: Either there is a missing 'override', or the member function 'GList::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:132:9: style:inconclusive: Either there is a missing 'override', or the member function 'GList::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:181:8: style: The member function 'GBitVec::bitSizeError' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:199:8: style:inconclusive: Technically the member function 'GBitVec::any' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:468:8: style: The member function 'GBitVec::NumBitWords' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:503:8: style: The member function 'GBitVec::init_words' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:118:9: style:inconclusive: Technically the member function 'GMapSeg::g_within' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:144:7: style:inconclusive: Technically the member function 'GffScore::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:147:7: style:inconclusive: Technically the member function 'GffScore::operator<=' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:150:7: style:inconclusive: Technically the member function 'GffScore::operator>' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:153:7: style:inconclusive: Technically the member function 'GffScore::operator>=' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:156:7: style:inconclusive: Technically the member function 'GffScore::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:195:19: debug: CheckClass::isMemberVar found used member variable 'fCount' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:198:15: debug: CheckClass::isMemberVar found used member variable 'fCount' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:199:15: debug: CheckClass::isMemberVar found used member variable 'fArray' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:199:38: debug: CheckClass::isMemberVar found used member variable 'fArray' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:200:16: debug: CheckClass::isMemberVar found used member variable 'fArray' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:200:41: debug: CheckClass::isMemberVar found used member variable 'fArray' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:193:10: style:inconclusive: Technically the member function 'GMapSegments::gmap' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:206:19: debug: CheckClass::isMemberVar found used member variable 'fCount' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:209:15: debug: CheckClass::isMemberVar found used member variable 'fCount' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:210:15: debug: CheckClass::isMemberVar found used member variable 'fArray' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.cpp:453:15: style: The member function 'GffLine::ensembl_GFF_ID_process' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:304:10: note: The member function 'GffLine::ensembl_GFF_ID_process' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:453:15: note: The member function 'GffLine::ensembl_GFF_ID_process' can be static.
gpertea-stringtie-4b2320a/gclib/gff.h:409:8: style:inconclusive: Technically the member function 'GffAttr::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:412:8: style:inconclusive: Technically the member function 'GffAttr::operator>' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:415:8: style:inconclusive: Technically the member function 'GffAttr::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:437:9: style:inconclusive: Technically the member function 'GffNameInfo::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:440:9: style:inconclusive: Technically the member function 'GffNameInfo::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:465:6: style:inconclusive: Either there is a missing 'override', or the member function 'GffNameList::lastNameId' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:502:6: style: Either there is a missing 'override', or the member function 'GffNameList::removeName' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:783:8: style:inconclusive: Technically the member function 'GffObj::hasErrors' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:785:8: style:inconclusive: Technically the member function 'GffObj::hasGffID' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:787:8: style:inconclusive: Technically the member function 'GffObj::createdByExon' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:789:8: style:inconclusive: Technically the member function 'GffObj::isCDSOnly' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:791:8: style:inconclusive: Technically the member function 'GffObj::isXCDS' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:793:8: style:inconclusive: Technically the member function 'GffObj::isFinalized' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:796:8: style:inconclusive: Technically the member function 'GffObj::isGene' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:798:8: style:inconclusive: Technically the member function 'GffObj::isDiscarded' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:800:8: style:inconclusive: Technically the member function 'GffObj::isUsed' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:802:8: style:inconclusive: Technically the member function 'GffObj::isTranscript' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:804:8: style:inconclusive: Technically the member function 'GffObj::isGeneSegment' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:806:8: style:inconclusive: Technically the member function 'GffObj::promotedChildren' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:811:8: style:inconclusive: Technically the member function 'GffObj::getUserFlags' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:813:8: style:inconclusive: Technically the member function 'GffObj::getLevel' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:928:16: style:inconclusive: Technically the member function 'GffObj::getSubfName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:940:9: style:inconclusive: Technically the member function 'GffObj::hasCDS' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:942:16: style:inconclusive: Technically the member function 'GffObj::getFeatureName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2644:13: style: The member function 'GffObj::removeExonAttr' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:952:8: note: The member function 'GffObj::removeExonAttr' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:2644:13: note: The member function 'GffObj::removeExonAttr' can be static.
gpertea-stringtie-4b2320a/gclib/gff.h:973:10: style: The member function 'GffObj::getExonAttr' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:987:16: style:inconclusive: Technically the member function 'GffObj::getGSeqName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:991:16: style:inconclusive: Technically the member function 'GffObj::getRefName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:996:16: style:inconclusive: Technically the member function 'GffObj::getTrackName' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1040:13: style: The member function 'GffObj::exonOverlapIdx' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:1025:8: note: The member function 'GffObj::exonOverlapIdx' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1040:13: note: The member function 'GffObj::exonOverlapIdx' can be static.
gpertea-stringtie-4b2320a/gclib/gff.h:1068:9: style:inconclusive: Technically the member function 'GffObj::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1146:9: style:inconclusive: Technically the member function 'GffObj::empty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1177:9: style:inconclusive: Technically the member function 'GSeqStat::operator>' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1180:9: style:inconclusive: Technically the member function 'GSeqStat::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1183:9: style:inconclusive: Technically the member function 'GSeqStat::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1445:18: style: The member function 'GffReader::gfoBuildId' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:1299:9: note: The member function 'GffReader::gfoBuildId' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1445:18: note: The member function 'GffReader::gfoBuildId' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1465:20: style: The member function 'GffReader::gfoAdd' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:1302:11: note: The member function 'GffReader::gfoAdd' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1465:20: note: The member function 'GffReader::gfoAdd' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1470:20: style: The member function 'GffReader::gfoReplace' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:1303:11: note: The member function 'GffReader::gfoReplace' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1470:20: note: The member function 'GffReader::gfoReplace' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1620:9: debug: CheckClass::isMemberVar found used member variable 'transcripts_Only' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1577:6: debug: CheckClass::isMemberVar found used member variable 'keep_Attrs' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1517:20: style: The member function 'GffReader::updateParent' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/gff.h:1324:11: note: The member function 'GffReader::updateParent' can be static.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1517:20: note: The member function 'GffReader::updateParent' can be static.
gpertea-stringtie-4b2320a/gclib/gff.h:1356:8: style:inconclusive: Technically the member function 'GffReader::procEnsemblID' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1358:8: style:inconclusive: Technically the member function 'GffReader::getSorting' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1367:8: style:inconclusive: Technically the member function 'GffReader::transcriptsOnly' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1372:8: style:inconclusive: Technically the member function 'GffReader::keepGenes' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1380:8: style:inconclusive: Technically the member function 'GffReader::showWarnings' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1728:6: debug: CheckClass::isMemberVar found used member variable 'is_BED' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1657:6: debug: CheckClass::isMemberVar found used member variable 'is_BED' with varid 0 [varid0]
gpertea-stringtie-4b2320a/gclib/gff.h:1453:9: style:inconclusive: Technically the member function 'GSegMatch::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/gff.h:1454:9: style:inconclusive: Technically the member function 'GSegMatch::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:64:10: style:inconclusive: Either there is a missing 'override', or the member function 'GArray < GSegMatch >::Sorted' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GList.hh:66:10: style:inconclusive: Either there is a missing 'override', or the member function 'GArray < GSegMatch >::Unique' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:213:10: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:214:10: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:215:9: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:216:9: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:229:9: note: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: note: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GVec.hh:213:10: style:inconclusive: Technically the member function 'GPVec < GeneCDSChain >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:214:10: style:inconclusive: Technically the member function 'GPVec < GeneCDSChain >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:215:9: style:inconclusive: Technically the member function 'GPVec < GeneCDSChain >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:216:9: style:inconclusive: Technically the member function 'GPVec < GeneCDSChain >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: style:inconclusive: Technically the member function 'GPVec < GeneCDSChain >::IndexOf' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:229:9: note: Technically the member function 'GPVec < GeneCDSChain >::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GVec.hh:776:38: note: Technically the member function 'GPVec < GeneCDSChain >::IndexOf' can be const.
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < GMapSeg >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < GMapSeg >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < GMapSeg >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < GMapSeg >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < GffExon >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < GffExon >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < GffExon >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < GffExon >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < GeneCDS >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < GeneCDS >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < GeneCDS >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < GeneCDS >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < int >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < int >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < int >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < int >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:94:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::Capacity' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:148:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:155:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::isEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GVec.hh:156:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::notEmpty' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:412:21: style:inconclusive: Either there is a missing 'override', or the member function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:412:21: style:inconclusive: Either there is a missing 'override', or the member function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:412:21: style:inconclusive: Either there is a missing 'override', or the member function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:382:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:165:21: style:inconclusive: Either there is a missing 'override', or the member function 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::getLastKey' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:80:17: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:88:17: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:97:14: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:111:14: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:115:14: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:119:6: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be static. [functionStatic]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:141:18: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Count' can be const. [functionConst]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:81:15: warning: Class 'GFaSeqGet' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/GFaSeqGet.h:81:15: warning: Class 'GFaSeqGet' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/gff.h:714:46: warning: Class 'GffExon' has dynamic memory/resource allocation(s). The operator= is explicitly defaulted but the default operator= does not work well. It is recommended to define or delete the operator=. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1346:24: warning: Class 'GffObj' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1346:24: warning: Class 'GffObj' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/gff.h:1244:6: warning: Class 'CNonExon' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1244:6: warning: Class 'CNonExon' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/gff.h:1401:7: warning: Class 'GffReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1401:7: warning: Class 'GffReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , int , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , int , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , int , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , int , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , int , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , int , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashSetCachedBucket < const char * , uint64_t > , KHashCachedHash < KHashSetCachedBucket < const char * , uint64_t > , uint64_t > , KHashCachedEq < KHashSetCachedBucket < const char * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashSetCachedBucket < const char * , uint64_t > , KHashCachedHash < KHashSetCachedBucket < const char * , uint64_t > , uint64_t > , KHashCachedEq < KHashSetCachedBucket < const char * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GffNameInfo * > , KHashMapHash < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GffNameInfo * > , KHashMapHash < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GeneCDSChain * > , KHashMapHash < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GeneCDSChain * > , KHashMapHash < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , int > , KHashMapHash < KHashMapBucket < const char * , int > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , int > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , int > , KHashMapHash < KHashMapBucket < const char * , int > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , int > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GPVec < GffObj > * > , KHashMapHash < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , GPVec < GffObj > * > , KHashMapHash < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , CNonExon * > , KHashMapHash < KHashMapBucket < const char * , CNonExon * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , CNonExon * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/gclib/khashl.hh:50:26: warning: Class 'KHashSet < KHashMapBucket < const char * , CNonExon * > , KHashMapHash < KHashMapBucket < const char * , CNonExon * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , CNonExon * > , GHashKey_Eq < const char * > > , uint64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , GffNameInfo * > , KHashMapHash < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , GffNameInfo * > , KHashMapHash < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GffNameInfo * > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , GeneCDSChain * > , KHashMapHash < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , GeneCDSChain * > , KHashMapHash < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GeneCDSChain * > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , int > , KHashMapHash < KHashMapBucket < const char * , int > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , int > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , int > , KHashMapHash < KHashMapBucket < const char * , int > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , int > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , GPVec < GffObj > * > , KHashMapHash < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , GPVec < GffObj > * > , KHashMapHash < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , GPVec < GffObj > * > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: warning: The class 'KHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapBucket < const char * , CNonExon * > , KHashMapHash < KHashMapBucket < const char * , CNonExon * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , CNonExon * > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapBucket < const char * , CNonExon * > , KHashMapHash < KHashMapBucket < const char * , CNonExon * > , GHashKey_wyHash < const char * > , uint64_t > , KHashMapEq < KHashMapBucket < const char * , CNonExon * > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:187:16: note: Derived function 'KHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:224:16: warning: The class 'KHashSetCached < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashSetCachedBucket < const char * , uint64_t > , KHashCachedHash < KHashSetCachedBucket < const char * , uint64_t > , uint64_t > , KHashCachedEq < KHashSetCachedBucket < const char * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashSetCachedBucket < const char * , uint64_t > , KHashCachedHash < KHashSetCachedBucket < const char * , uint64_t > , uint64_t > , KHashCachedEq < KHashSetCachedBucket < const char * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:224:16: note: Derived function 'KHashSetCached < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GffNameInfo * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GeneCDSChain * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , int , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , int , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , int , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , int , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , int , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , int , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , GPVec < GffObj > * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: warning: The class 'KHashMapCached < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'key' also defined in its parent class 'KHashSet < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/khashl.hh:54:12: note: Parent function 'KHashSet < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , KHashCachedHash < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , uint64_t > , KHashCachedEq < KHashMapCachedBucket < const char * , CNonExon * , uint64_t > , GHashKey_Eq < const char * > > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/khashl.hh:251:16: note: Derived function 'KHashMapCached < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::key'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:152:13: warning: The class 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Add' also defined in its parent class 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:80:17: note: Parent function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:152:13: note: Derived function 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:167:6: warning: The class 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:88:17: note: Parent function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:167:6: note: Derived function 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:179:14: warning: The class 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:97:14: note: Parent function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:179:14: note: Derived function 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:190:14: warning: The class 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Reset' also defined in its parent class 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:101:14: note: Parent function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:190:14: note: Derived function 'GStrSet < GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Add' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: warning: The class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Reset' also defined in its parent class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:269:14: note: Parent function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: note: Derived function 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Add' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: warning: The class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Reset' also defined in its parent class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:269:14: note: Parent function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: note: Derived function 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Add' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:398:13: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:416:2: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Remove' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:431:2: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:445:3: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Clear' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:267:3: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:458:3: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: warning: The class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' defines member function with name 'Reset' also defined in its parent class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >'. [duplInheritedMember]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:269:14: note: Parent function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:468:14: note: Derived function 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Reset'
gpertea-stringtie-4b2320a/gclib/GList.hh:94:5: style: Class 'GList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:143:3: style: Class 'GBitVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:82:2: style: Struct 'TOvlData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:116:2: style: Class 'GMapSeg' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:135:2: style: Struct 'GffScore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:168:2: style: Class 'GMapSegments' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:236:5: style: Class 'BEDLine' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:377:3: style: Class 'GffAttr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:429:4: style: Class 'GffNameInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:460:3: style: Class 'GffNameList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:691:3: style: Class 'GffExon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:694:3: style: Class 'GffExon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:857:3: style: Class 'GffObj' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:882:4: style: Class 'GffObj' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1168:4: style: Class 'GSeqStat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1204:4: style: Class 'GfList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1329:3: style: Class 'GffReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1391:3: style: Class 'GffReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1455:4: style: Class 'GSegMatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.h:1462:2: style: Class 'GeneCDS' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:32:5: style: Class 'GArray < GSegMatch >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GList.hh:33:5: style: Class 'GArray < GSegMatch >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:180:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:181:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:184:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:180:5: style: Class 'GPVec < GeneCDSChain >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:181:5: style: Class 'GPVec < GeneCDSChain >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:184:5: style: Class 'GPVec < GeneCDSChain >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < GMapSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < GffExon >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < GeneCDS >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GVec.hh:43:5: style: Class 'GVec < GPVec < GffObj > * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:394:2: style: Class 'GHash < int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:394:2: style: Class 'GHash < GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:394:2: style: Class 'GHash < CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/GHashMap.hh:280:2: style: Class 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/gclib/gff.cpp:708:11: style: Condition 'validCDS' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:707:16: note: Assignment 'validCDS=true', assigned value is 1
gpertea-stringtie-4b2320a/gclib/gff.cpp:708:11: note: Condition 'validCDS' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:1236:14: style: Condition 'CDstart>0' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1233:23: note: Assuming that condition 'bedline.cds_start>0' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:1234:18: note: Assignment 'CDstart=bedline.cds_start', assigned value is greater than 0
gpertea-stringtie-4b2320a/gclib/gff.cpp:1236:14: note: Condition 'CDstart>0' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:2801:39: style: Condition 'g_start<=sgend' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2800:36: note: Assuming that condition 'g_start>sgend' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:2801:39: note: Condition 'g_start<=sgend' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:2831:38: style: Condition 'g_start<=sgend' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2830:35: note: Assuming that condition 'g_start>sgend' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:2831:38: note: Condition 'g_start<=sgend' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:3218:40: style: Condition 'CDstart<=sgend' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3217:37: note: Assuming that condition 'CDstart>sgend' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:3218:40: note: Condition 'CDstart<=sgend' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:3238:39: style: Condition 'CDstart<=sgend' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3237:36: note: Assuming that condition 'CDstart>sgend' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:3238:39: note: Condition 'CDstart<=sgend' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:3407:81: style: Condition '(eqcode=singleExonTMatch(m,r,odta.ovlen,trange,&odta.ovlRefstart))>0' is always false [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3407:34: note: Calling function 'singleExonTMatch' returns 0
gpertea-stringtie-4b2320a/gclib/gff.cpp:3407:81: note: Condition '(eqcode=singleExonTMatch(m,r,odta.ovlen,trange,&odta.ovlRefstart))>0' is always false
gpertea-stringtie-4b2320a/gclib/gff.cpp:3538:28: style: Condition 'm.exons[imax]->start<=r.exons[0]->end' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3534:27: note: Assuming that condition 'm.exons[imax]->start<r.exons[0]->end' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:3538:28: note: Condition 'm.exons[imax]->start<=r.exons[0]->end' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:3554:20: style: Condition 'm.exons[0]->end>=r.exons[jmax]->start' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3549:32: note: Assuming that condition 'r.exons[jmax]->start<m.exons[0]->end' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:3554:20: note: Condition 'm.exons[0]->end>=r.exons[jmax]->start' is always true
gpertea-stringtie-4b2320a/gclib/gff.cpp:2443:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2443:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2454:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2859:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2859:2: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2903:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2903:2: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2931:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2931:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2950:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2950:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3103:5: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3103:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3118:4: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3118:4: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3140:21: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3140:21: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2181:6: warning: Either the condition 'gfr!=NULL' is redundant or there is possible null pointer dereference: gfr. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2250:13: note: Assuming that condition 'gfr!=NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:2181:6: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/gff.cpp:2224:25: warning: Either the condition 'gfr!=NULL' is redundant or there is possible null pointer dereference: gfr. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2250:13: note: Assuming that condition 'gfr!=NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:2224:25: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/gff.cpp:2243:7: warning: Either the condition 'gfr!=NULL' is redundant or there is possible null pointer dereference: gfr. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2250:13: note: Assuming that condition 'gfr!=NULL' is not redundant
gpertea-stringtie-4b2320a/gclib/gff.cpp:2243:7: note: Null pointer dereference
gpertea-stringtie-4b2320a/gclib/GBitVec.h:126:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:151:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:166:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:171:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:451:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:455:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBitVec.h:499:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:238:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:239:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:298:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:301:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:324:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:326:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:334:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:337:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:357:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:358:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:359:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:360:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:361:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:362:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:363:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:382:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:386:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:434:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:917:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:918:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:919:8: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1094:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1098:9: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1103:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1333:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1402:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1416:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.h:1417:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:73:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:74:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:91:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:92:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:111:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:112:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:138:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:139:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:171:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:172:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:266:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:268:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:325:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:326:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:375:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:376:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:401:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:403:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:457:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:462:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:473:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:474:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:485:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:487:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:630:28: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:696:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:698:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:727:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:733:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:753:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:879:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1449:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1626:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1636:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1712:2: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1916:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1971:23: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1973:23: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2010:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2015:7: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2095:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2107:6: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2179:4: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2683:5: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2767:3: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3091:10: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GList.hh:601:8: style: Variable 'idx' is reassigned a value before the old one has been used. [redundantAssignment]
gpertea-stringtie-4b2320a/gclib/GList.hh:572:5: note: idx is assigned
gpertea-stringtie-4b2320a/gclib/GList.hh:601:8: note: idx is overwritten
gpertea-stringtie-4b2320a/gclib/gff.cpp:66:21: style: The scope of the variable 'extbl' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:755:8: style: The scope of the variable 'i' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1843:11: style: The scope of the variable 'i' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2000:10: style: The scope of the variable 'same_aval' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2046:7: style: The scope of the variable 'i' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2330:9: style: The scope of the variable 'j' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2438:7: style: The scope of the variable 'dbuf' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3663:6: style: The scope of the variable 'l_iovh' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3664:6: style: The scope of the variable 'r_iovh' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3668:6: style: The scope of the variable 'l_jovh' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3669:6: style: The scope of the variable 'r_jovh' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GVec.hh:336:7: style: The scope of the variable 'c' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/GVec.hh:142:10: style: The scope of the variable 'v' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/gclib/gff.cpp:186:79: style:inconclusive: Function 'extractGFFAttr' argument 3 names different: declaration 'pre' definition 'attr'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/gff.h:306:80: note: Function 'extractGFFAttr' argument 3 names different: declaration 'pre' definition 'attr'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:186:79: note: Function 'extractGFFAttr' argument 3 names different: declaration 'pre' definition 'attr'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:261:29: style:inconclusive: Function 'BEDLine' argument 1 names different: declaration 'r' definition 'reader'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/gff.h:236:24: note: Function 'BEDLine' argument 1 names different: declaration 'r' definition 'reader'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:261:29: note: Function 'BEDLine' argument 1 names different: declaration 'r' definition 'reader'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1517:41: style:inconclusive: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/gff.h:1324:32: note: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:1517:41: note: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:574:47: style:inconclusive: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:184:23: note: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:574:47: note: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:574:47: style:inconclusive: Function 'GPVec < GeneCDSChain >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/gclib/GVec.hh:184:23: note: Function 'GPVec < GeneCDSChain >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/GVec.hh:574:47: note: Function 'GPVec < GeneCDSChain >' argument 1 names different: declaration 'list' definition 'plist'.
gpertea-stringtie-4b2320a/gclib/gff.cpp:385:10: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:292:9: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:385:10: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:426:10: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:419:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:426:10: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:704:12: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:515:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:704:12: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:755:8: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:491:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:755:8: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:3711:14: style: Local variable 'j' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3567:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:3711:14: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:3728:14: style: Local variable 'j' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3567:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:3728:14: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:3756:14: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3566:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:3756:14: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/gff.cpp:3772:14: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3566:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/gclib/gff.cpp:3772:14: note: Shadow variable
gpertea-stringtie-4b2320a/gclib/GVec.hh:152:35: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
gpertea-stringtie-4b2320a/gclib/GVec.hh:245:64: performance: Function parameter 'init_val' should be passed by const reference. [passedByValue]
gpertea-stringtie-4b2320a/gclib/GVec.hh:500:65: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
gpertea-stringtie-4b2320a/gclib/gff.h:144:27: style: Parameter 'v' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:147:28: style: Parameter 'v' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:150:27: style: Parameter 'v' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:153:28: style: Parameter 'v' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:156:28: style: Parameter 'v' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:409:28: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:412:27: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:415:27: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:437:33: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:440:32: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1068:28: style: Parameter 'd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1177:29: style: Parameter 'g' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1180:29: style: Parameter 'g' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1183:30: style: Parameter 'g' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1453:30: style: Parameter 'o' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.h:1454:31: style: Parameter 'o' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.cpp:949:33: style: Parameter 'reader' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3345:31: style: Parameter 'm' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3345:42: style: Parameter 'r' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.cpp:171:11: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:172:11: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:261:29: style: Parameter 'reader' can be declared as pointer to const. However it seems that 'BEDLine' is a callback function, if 'reader' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gpertea-stringtie-4b2320a/gclib/gff.h:220:7: note: You might need to cast the function pointer here
gpertea-stringtie-4b2320a/gclib/gff.cpp:261:29: note: Parameter 'reader' can be declared as pointer to const
gpertea-stringtie-4b2320a/gclib/gff.cpp:419:8: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:542:10: style: Variable 'pde' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1175:34: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1387:8: style: Variable 'l' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1470:73: style: Parameter 'toreplace' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1616:45: style: Parameter 'gffline' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1640:58: style: Parameter 'subp_name' can be declared as pointer to const [constParameterReference]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1981:9: style: Variable 'attr_name' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1982:9: style: Variable 'attr_val' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1987:11: style: Variable 'ov' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1999:11: style: Variable 't_val' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2095:12: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2541:8: style: Variable 'prod' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3010:9: style: Variable 'gid' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3150:10: style: Variable 'g_id' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.h:498:18: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/gclib/gff.h:1125:46: style: Parameter 'tlabel' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/gclib/GVec.hh:145:22: error: Uninitialized variable: v [uninitvar]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1747:13: style: Variable 'prevseen' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:1820:18: style: Variable 'found_parent' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2000:19: style: Variable 'same_aval' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2046:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:2492:12: style: Variable 'pch' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3382:11: style: Variable 'result' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/gff.cpp:3386:11: style: Variable 'result' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/gclib/GVec.hh:142:10: style: Variable 'v' is not assigned a value. [unassignedVariable]
gpertea-stringtie-4b2320a/gclib/proc_mem.cpp:45:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:104:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:163:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:222:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREAD2 [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:240:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:251:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:290:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:436:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:625:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:644:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:662:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FSECONDARY [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:1312:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:2125:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:2598:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable predno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:2814:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:3101:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable keep [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:3147:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable future [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:3318:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable future [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:3609:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:4380:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ngraph [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:4479:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ngraph [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:4623:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:5177:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable g [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:5396:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable contnode [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:5827:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guide [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:6922:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable real [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7009:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pattern [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7083:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable abundance [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7165:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable g [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7272:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7443:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pattern [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7494:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7546:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable real [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:7751:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable abundance [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9187:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9522:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodes [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9785:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9899:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9939:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:9965:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guide [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:10424:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:10510:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:10722:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guide [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:11132:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable guide [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:11456:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:11731:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:11844:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:11860:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trf [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12317:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodes [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12565:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pattern [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12580:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pat [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12591:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodes [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12752:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:12770:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable g [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:13100:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trf [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:13602:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nodes [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:14110:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:14125:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:14149:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:14261:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:16082:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:16906:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17322:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17397:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17481:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17525:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17598:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17639:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17666:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17692:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable predno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17822:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17842:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17850:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable predno [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17858:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:17894:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18039:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18075:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18263:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18324:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable exoncov [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18384:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:18450:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:19572:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:19657:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:19866:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:19955:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:20114:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/rlink.cpp:97:15: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
gpertea-stringtie-4b2320a/rlink.cpp:113:14: style: The member function 'OvlTracker::get_index' can be static. [functionStatic]
gpertea-stringtie-4b2320a/rlink.h:331:33: warning: Struct 'CComponent' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/rlink.h:331:33: warning: Struct 'CComponent' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/rlink.h:60:2: style: Struct 'CBundlenode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:70:2: style: Struct 'CPath' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:93:2: style: Struct 'CTransfrag' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:103:2: style: Struct 'CMTransfrag' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:112:2: style: Struct 'CGuide' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:125:2: style: Struct 'CPartGuide' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:152:2: style: Struct 'CGroup' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:160:2: style: Struct 'CMerge' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:168:2: style: Struct 'CExon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:175:2: style: Struct 'CPred' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:182:2: style: Struct 'CLongTrf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:190:2: style: Struct 'CMPrediction' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:198:2: style: Struct 'CNodeCapacity' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:209:9: style: Struct 'CGene' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:217:2: style: Struct 'CGraphinfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:225:2: style: Struct 'CGJunc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:235:2: style: Struct 'CGNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:243:2: style: Struct 'CTreePat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:272:2: style: Struct 'CTrimPoint' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:279:2: style: Struct 'CInterval' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:287:2: style: Struct 'CMaxIntv' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:295:2: style: Struct 'CNasc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:302:2: style: Struct 'CNascIntv' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:317:2: style: Struct 'CTrInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:324:2: style: Struct 'CNetEdge' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:330:2: style: Struct 'CComponent' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:345:2: style: Struct 'GEdge' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.h:367:5: style: Struct 'CGraphnode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.cpp:121:3: style: Class 'OvlTracker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/rlink.cpp:9724:7: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
gpertea-stringtie-4b2320a/rlink.cpp:9722:11: note: outer condition: pos
gpertea-stringtie-4b2320a/rlink.cpp:9724:7: note: identical inner condition: pos
gpertea-stringtie-4b2320a/rlink.cpp:19381:8: style: The if condition is the same as the previous if condition [duplicateCondition]
gpertea-stringtie-4b2320a/rlink.cpp:19374:8: note: First condition
gpertea-stringtie-4b2320a/rlink.cpp:19381:8: note: Second condition
gpertea-stringtie-4b2320a/rlink.cpp:7527:7: style: The statement 'if (!exonovlp) exonovlp=true' is logically equivalent to 'exonovlp=true'. [duplicateConditionalAssign]
gpertea-stringtie-4b2320a/rlink.cpp:7527:26: note: Assignment 'exonovlp=true'
gpertea-stringtie-4b2320a/rlink.cpp:7527:7: note: Condition '!exonovlp' is redundant
gpertea-stringtie-4b2320a/rlink.cpp:806:23: style: Condition 'longr' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:789:12: note: Assuming that condition 'longr' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:806:23: note: Condition 'longr' is always true
gpertea-stringtie-4b2320a/rlink.cpp:7122:11: style: Condition '!firstex' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:7117:19: note: Assuming that condition 'firstex' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:7122:11: note: Condition '!firstex' is always true
gpertea-stringtie-4b2320a/rlink.cpp:7196:11: style: Condition '!firstex' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:7191:19: note: Assuming that condition 'firstex' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:7196:11: note: Condition '!firstex' is always true
gpertea-stringtie-4b2320a/rlink.cpp:9794:11: style: Condition '!firstex' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:9782:19: note: Assuming that condition 'firstex' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:9794:11: note: Condition '!firstex' is always true
gpertea-stringtie-4b2320a/rlink.cpp:10783:11: style: Condition 'pos' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:11013:10: style: Condition 'pos!=NULL' is always false [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:11010:8: note: Assignment 'pos=NULL', assigned value is 0
gpertea-stringtie-4b2320a/rlink.cpp:11013:10: note: Condition 'pos!=NULL' is always false
gpertea-stringtie-4b2320a/rlink.cpp:11193:10: style: Condition 'pos' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:11744:11: style: Condition '!firstex' is always true [knownConditionTrueFalse]
gpertea-stringtie-4b2320a/rlink.cpp:11714:19: note: Assuming that condition 'firstex' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:11744:11: note: Condition '!firstex' is always true
gpertea-stringtie-4b2320a/rlink.cpp:19402:4: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/rlink.cpp:20317:6: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/rlink.cpp:9931:16: warning: Either the condition 't' is redundant or there is possible null pointer dereference: t. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/rlink.cpp:9948:6: note: Assuming that condition 't' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:9931:16: note: Null pointer dereference
gpertea-stringtie-4b2320a/rlink.cpp:9939:83: warning: Either the condition 't' is redundant or there is possible null pointer dereference: t. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/rlink.cpp:9948:6: note: Assuming that condition 't' is not redundant
gpertea-stringtie-4b2320a/rlink.cpp:9939:83: note: Null pointer dereference
gpertea-stringtie-4b2320a/rlink.cpp:64:25: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:65:25: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1098:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1099:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1106:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1107:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1114:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1115:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1130:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1131:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1145:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1146:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1157:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1158:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1181:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1182:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1197:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1198:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1207:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1208:16: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1217:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1218:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1229:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1230:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1237:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:1238:15: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:3125:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:3126:12: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:7249:18: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:7250:18: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:14318:21: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:15522:26: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17281:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17282:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17298:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17299:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17343:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17344:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17353:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17354:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17362:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17363:11: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17372:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:17373:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:19397:13: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:20317:86: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/rlink.cpp:10469:89: style: Floating-point cast causes loss of precision. [suspiciousFloatingPointCast]
gpertea-stringtie-4b2320a/rlink.cpp:10473:36: style: Floating-point cast causes loss of precision. [suspiciousFloatingPointCast]
gpertea-stringtie-4b2320a/rlink.cpp:5854:15: style: Variable 't->longread' is reassigned a value before the old one has been used. [redundantAssignment]
gpertea-stringtie-4b2320a/rlink.cpp:5843:16: note: t->longread is assigned
gpertea-stringtie-4b2320a/rlink.cpp:5854:15: note: t->longread is overwritten
gpertea-stringtie-4b2320a/rlink.cpp:16121:6: style: Variable 'nj' is reassigned a value before the old one has been used. [redundantAssignment]
gpertea-stringtie-4b2320a/rlink.cpp:16119:6: note: nj is assigned
gpertea-stringtie-4b2320a/rlink.cpp:16121:6: note: nj is overwritten
gpertea-stringtie-4b2320a/rlink.cpp:268:16: style: The scope of the variable 'num_matches' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:664:20: style: The scope of the variable 'junction' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:3804:15: style: The scope of the variable 'istart' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:6043:12: style: The scope of the variable 'rightdist' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:6423:13: style: The scope of the variable 'rightdist' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:6880:10: style: The scope of the variable 'abundance' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:6881:7: style: The scope of the variable 't0' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:6945:8: style: The scope of the variable 'comp' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8070:16: style: The scope of the variable 'maxcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8074:6: style: The scope of the variable 'nextnode' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8121:32: style: The scope of the variable 'childcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8122:8: style: The scope of the variable 'tchild' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8288:12: style: The scope of the variable 'maxcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8292:6: style: The scope of the variable 'nextnode' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8341:32: style: The scope of the variable 'parentcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8342:8: style: The scope of the variable 'tpar' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8510:10: style: The scope of the variable 'childcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:8674:10: style: The scope of the variable 'parentcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:10116:16: style: The scope of the variable 'flux' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:10676:10: style: The scope of the variable 'abundin' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:10677:10: style: The scope of the variable 'abundout' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:10986:9: style: The scope of the variable 'flux' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:11081:10: style: The scope of the variable 'abundin' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:11082:10: style: The scope of the variable 'abundout' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:12788:10: style: The scope of the variable 'include' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:12810:11: style: The scope of the variable 'include' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:14183:21: style: The scope of the variable 'feature' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:14921:12: style: The scope of the variable 'searchjunc' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:14922:12: style: The scope of the variable 'addjunction' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:15663:14: style: The scope of the variable 'g' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:18318:9: style: The scope of the variable 'intcov' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:19204:8: style: The scope of the variable 'runoff' can be reduced. [variableScope]
gpertea-stringtie-4b2320a/rlink.cpp:3411:10: style: Local variable 'n' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3280:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:3411:10: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:3458:10: style: Local variable 'n' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3280:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:3458:10: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:3521:10: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3365:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:3521:10: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:3816:18: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3785:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:3816:18: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4037:17: style: Local variable 'end' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3661:10: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4037:17: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4108:15: style: Local variable 'end' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:3661:10: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4108:15: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4707:13: style: Local variable 'trim' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4707:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4730:13: style: Local variable 'trim' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4730:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4762:13: style: Local variable 'trim' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4762:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:4785:13: style: Local variable 'trim' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:4785:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:5380:12: style: Local variable 'pos' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:5363:9: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:5380:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:5463:12: style: Local variable 'conflict' shadows outer function [shadowFunction]
gpertea-stringtie-4b2320a/rlink.cpp:5262:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:5463:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:5549:11: style: Local variable 'n' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:5440:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:5549:11: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:8947:11: style: Local variable 'j' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:8907:11: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:8947:11: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:11968:13: style: Local variable 'j' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:11952:9: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:11968:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:12421:12: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:12377:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:12421:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:12832:9: style: Local variable 'ng' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:12767:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:12832:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:13040:9: style: Local variable 'ng' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:12767:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:13040:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15107:21: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:14850:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15107:21: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15236:9: style: Local variable 'grcol' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:15213:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15236:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15269:9: style: Local variable 'grcol' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:15213:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15269:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15518:13: style: Local variable 'g' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:15497:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15518:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15663:14: style: Local variable 'g' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:15497:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15663:14: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:15914:17: style: Local variable 'g' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:15497:6: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:15914:17: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:16179:9: style: Local variable 'grcol' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:16157:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:16179:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:16210:9: style: Local variable 'grcol' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:16157:7: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:16210:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:16960:17: style: Local variable 'jn' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:16947:16: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:16960:17: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18052:9: style: Local variable 'exon' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18046:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18052:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18236:18: style: Local variable 'exoncov' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18198:10: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18236:18: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18498:13: style: Local variable 'start' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18490:12: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18498:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18500:13: style: Local variable 'end' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18492:12: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18500:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18539:9: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18424:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18539:9: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18581:13: style: Local variable 'start' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18573:12: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18581:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18583:13: style: Local variable 'end' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18575:12: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18583:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18648:13: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18424:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18648:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18811:14: style: Local variable 'lowcov' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.h:38:13: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18811:14: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18872:19: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18424:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18872:19: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:18968:12: style: Local variable 'ex' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18466:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:18968:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:19045:13: style: Local variable 'ex' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18466:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:19045:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:19199:7: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18424:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:19199:7: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:19443:18: style: Local variable 'p' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18424:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:19443:18: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:19472:12: style: Local variable 'geneid' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19404:9: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:19472:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:19473:12: style: Local variable 'trid' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:19405:9: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:19473:12: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:20234:13: style: Local variable 'i' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:20218:11: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:20234:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:20932:11: style: Local variable 'm' shadows outer variable [shadowVariable]
gpertea-stringtie-4b2320a/rlink.cpp:20526:8: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:20932:11: note: Shadow variable
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gpertea-stringtie-4b2320a/rlink.cpp:21104:11: note: Shadowed declaration
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gpertea-stringtie-4b2320a/rlink.cpp:21163:11: note: Shadowed declaration
gpertea-stringtie-4b2320a/rlink.cpp:21179:13: note: Shadow variable
gpertea-stringtie-4b2320a/rlink.cpp:144:39: style: Parameter 'rd' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1281:98: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1750:34: style: Parameter 'winleft' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1750:58: style: Parameter 'winright' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1766:35: style: Parameter 'winleft' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1766:59: style: Parameter 'winright' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1784:33: style: Parameter 'wincov' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:1813:35: style: Parameter 'wincov' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:3097:68: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4355:20: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4355:67: style: Parameter 'merge' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4456:20: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4456:67: style: Parameter 'merge' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4550:53: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4635:55: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4635:85: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:4872:66: style: Parameter 'group' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5142:91: style: Parameter 'group' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5206:61: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5206:91: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5262:42: style: Parameter 'trnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5262:74: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5262:92: style: Parameter 'trpat' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5262:122: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5351:68: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5351:94: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5431:83: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5431:116: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5596:56: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5596:117: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:5771:17: style: Variable 'guides' can be declared as reference to const [constVariableReference]
gpertea-stringtie-4b2320a/rlink.cpp:7065:74: style: Parameter 'mgt' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7066:22: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7066:83: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7066:107: style: Parameter 'guides' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7142:84: style: Parameter 'mgt' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7143:22: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7143:83: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7143:107: style: Parameter 'guides' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7291:57: style: Parameter 'pathpattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7291:106: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7292:18: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7329:106: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7330:18: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7508:57: style: Parameter 'p2' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7508:83: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7520:43: style: Parameter 'p1' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7737:50: style: Parameter 'compatible' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7810:27: style: Parameter 'trpattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7810:113: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7811:18: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7863:22: style: Parameter 'trpattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7863:59: style: Parameter 'pathpattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7863:108: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7864:18: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7926:63: style: Parameter 'trnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7947:51: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7947:118: style: Parameter 'pathincov' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7977:50: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:7978:16: style: Parameter 'pathoutcov' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:8007:38: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:8007:67: style: Parameter 'nodecov' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:8007:94: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:8795:89: style: Parameter 'node2path' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:8864:87: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9075:86: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9076:58: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9377:91: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9377:120: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9500:99: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9501:22: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9689:22: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9689:89: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9877:86: style: Parameter 'nodeflux' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:9878:22: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11382:101: style: Parameter 'transfrag' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11383:41: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11667:67: style: Parameter 'geneno' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11667:107: style: Parameter 'nodeflux' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11668:21: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11890:18: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:11890:42: style: Parameter 'no2gnode' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12126:104: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12196:112: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12554:62: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12563:40: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12563:73: style: Parameter 'guidetrf' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12577:29: style: Parameter 'pat' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:12587:51: style: Parameter 'gpos' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:14108:37: style: Parameter 'readlist' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17383:37: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17472:40: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17472:74: style: Parameter 'lowintron' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17502:40: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17592:37: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17689:41: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17820:35: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17840:45: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:17874:71: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:18069:48: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:18403:37: style: Parameter 'hashgene' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:19570:35: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:19831:45: style: Parameter 'pred' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/rlink.cpp:97:13: style: Variable 't' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:487:21: style: Variable 'tf' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1028:28: style: Parameter 'prevgroup' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:1058:34: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:1084:50: style: Parameter 'group' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:1098:11: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1099:11: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1106:11: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1107:11: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1181:14: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1182:14: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1197:14: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1198:14: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1237:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1238:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:1732:88: style: Parameter 'bundlenode' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:1842:60: style: Parameter 'bpcov' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:2901:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:2946:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:3000:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:3080:54: style: Parameter 'guidecov' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:3125:10: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:3126:10: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4245:18: style: Variable 'prevnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4273:10: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4287:10: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4455:91: style: Parameter 'rprop' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:4457:46: style: Parameter 'graphno' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:4457:65: style: Parameter 'edgeno' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:4506:18: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4565:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4642:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4714:16: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4737:16: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4769:16: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4792:16: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4835:11: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:4871:46: style: Parameter 'graphno' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:4871:65: style: Parameter 'edgeno' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:5009:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5018:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5055:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5062:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5070:17: style: Variable 'gnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5116:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5123:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5213:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5279:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5363:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5380:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5466:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5484:15: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5491:15: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5596:26: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:5745:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5858:10: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5924:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:5930:8: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:6742:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:6824:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:6835:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7014:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7035:11: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7105:14: style: Variable 'prevnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7179:14: style: Variable 'prevnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7216:29: style: Parameter 'capacity' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:7216:51: style: Parameter 'flow' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:7291:31: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:7305:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7316:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7399:8: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7406:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7413:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7421:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7428:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7512:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7563:11: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7657:11: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7814:7: style: Variable 'edgep' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7847:9: style: Variable 'edget' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7878:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:7889:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8091:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8200:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8248:7: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8311:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8421:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8471:7: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8527:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8564:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8639:7: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8692:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8734:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8784:7: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:8805:36: style: Parameter 'capacity' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:8805:58: style: Parameter 'flow' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:9187:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:9696:14: style: Variable 'prevnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:9721:8: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10103:8: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10169:17: style: Variable 'epos0' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10173:17: style: Variable 'epos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10208:16: style: Variable 'epos0' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10212:16: style: Variable 'epos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10243:15: style: Variable 'epos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10248:15: style: Variable 'epos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:10779:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11007:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11189:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11456:14: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11672:14: style: Variable 'prevnode' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11917:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11925:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11963:11: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:11972:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12166:10: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12177:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12219:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12225:12: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12322:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12338:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12401:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12477:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12569:8: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12646:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12663:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12683:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:12707:9: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:13130:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:13136:13: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:16834:17: style: Variable 'jp' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17281:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17282:15: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17353:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17354:15: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17362:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17363:9: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17409:13: style: Variable 'lastinterv' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17425:13: style: Variable 'lastinterv' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:17855:52: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:18478:10: style: Variable 'gi' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:18559:11: style: Variable 'gi' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:18736:11: style: Variable 'gi' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/rlink.cpp:19605:48: style: Parameter 'p2' can be declared as pointer to const [constParameterPointer]
gpertea-stringtie-4b2320a/rlink.cpp:3424:10: style: Variable 'nnode' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:6945:12: style: Variable 'comp' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:10986:13: style: Variable 'flux' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:11012:7: style: Variable 'key' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:11855:8: style: Variable 'pn' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:12420:13: style: Variable 'previ' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:12495:13: style: Variable 'nexti' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:13625:3: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:14674:20: style: Variable 'support' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:14768:20: style: Variable 'support' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:16121:6: style: Variable 'nj' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18318:15: style: Variable 'intcov' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/rlink.cpp:18660:10: style: Variable 'pintv' is assigned a value that is never used. [unreadVariable]
gpertea-stringtie-4b2320a/stringtie.cpp:342:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/stringtie.cpp:1001:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/stringtie.cpp:1428:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/stringtie.cpp:991:15: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
gpertea-stringtie-4b2320a/tmerge.h:13:7: style:inconclusive: Technically the member function 'TInputRecord::operator<' can be const. [functionConst]
gpertea-stringtie-4b2320a/tmerge.h:35:7: style:inconclusive: Technically the member function 'TInputRecord::operator==' can be const. [functionConst]
gpertea-stringtie-4b2320a/tmerge.h:44:10: warning: Struct 'TInputRecord' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
gpertea-stringtie-4b2320a/tmerge.h:44:10: warning: Struct 'TInputRecord' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
gpertea-stringtie-4b2320a/tmerge.h:42:2: style: Struct 'TInputRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
gpertea-stringtie-4b2320a/stringtie.cpp:419:11: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/stringtie.cpp:413:17: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/stringtie.cpp:413:17: note: Assignment 'f=std::fopen(ptff.chars(),"r")', assigned value is 0
gpertea-stringtie-4b2320a/stringtie.cpp:419:11: note: Null pointer dereference
gpertea-stringtie-4b2320a/stringtie.cpp:626:18: warning: Either the condition 'faseq==NULL' is redundant or there is possible null pointer dereference: faseq. [nullPointerRedundantCheck]
gpertea-stringtie-4b2320a/stringtie.cpp:623:14: note: Assuming that condition 'faseq==NULL' is not redundant
gpertea-stringtie-4b2320a/stringtie.cpp:626:18: note: Null pointer dereference
gpertea-stringtie-4b2320a/stringtie.cpp:897:11: warning: If resource allocation fails, then there is a possible null pointer dereference: g_out [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/stringtie.cpp:894:14: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/stringtie.cpp:894:14: note: Assignment 'g_out=std::fopen(genefname.chars(),"w")', assigned value is 0
gpertea-stringtie-4b2320a/stringtie.cpp:897:11: note: Null pointer dereference
gpertea-stringtie-4b2320a/stringtie.cpp:489:38: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/stringtie.cpp:1555:35: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/stringtie.cpp:1554:32: style: Parameter 'td' can be declared as reference to const. However it seems that 'workerThread' is a callback function, if 'td' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gpertea-stringtie-4b2320a/stringtie.cpp:489:24: note: You might need to cast the function pointer here
gpertea-stringtie-4b2320a/stringtie.cpp:1554:32: note: Parameter 'td' can be declared as reference to const
gpertea-stringtie-4b2320a/stringtie.cpp:991:13: style: Variable 't' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/stringtie.cpp:1695:16: style: Variable 'g' can be declared as pointer to const [constVariablePointer]
gpertea-stringtie-4b2320a/tablemaker.cpp:34:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/tablemaker.cpp:11:8: style:inconclusive: Technically the member function 'COvlSorter::operator()' can be const. [functionConst]
gpertea-stringtie-4b2320a/tablemaker.cpp:157:4: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/tablemaker.cpp:157:4: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/tablemaker.cpp:162:4: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/tablemaker.cpp:162:4: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gpertea-stringtie-4b2320a/tablemaker.cpp:206:64: style:inconclusive: Function 'rc_addFeatures' argument 2 names different: declaration 'fexons' definition 'exonSet'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/tablemaker.h:150:55: note: Function 'rc_addFeatures' argument 2 names different: declaration 'fexons' definition 'exonSet'.
gpertea-stringtie-4b2320a/tablemaker.cpp:206:64: note: Function 'rc_addFeatures' argument 2 names different: declaration 'fexons' definition 'exonSet'.
gpertea-stringtie-4b2320a/tablemaker.cpp:206:92: style:inconclusive: Function 'rc_addFeatures' argument 3 names different: declaration 'edata' definition 'exonTable'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/tablemaker.h:150:82: note: Function 'rc_addFeatures' argument 3 names different: declaration 'edata' definition 'exonTable'.
gpertea-stringtie-4b2320a/tablemaker.cpp:206:92: note: Function 'rc_addFeatures' argument 3 names different: declaration 'edata' definition 'exonTable'.
gpertea-stringtie-4b2320a/tablemaker.cpp:207:54: style:inconclusive: Function 'rc_addFeatures' argument 5 names different: declaration 'fintrons' definition 'intronSet'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/tablemaker.h:151:57: note: Function 'rc_addFeatures' argument 5 names different: declaration 'fintrons' definition 'intronSet'.
gpertea-stringtie-4b2320a/tablemaker.cpp:207:54: note: Function 'rc_addFeatures' argument 5 names different: declaration 'fintrons' definition 'intronSet'.
gpertea-stringtie-4b2320a/tablemaker.cpp:207:84: style:inconclusive: Function 'rc_addFeatures' argument 6 names different: declaration 'idata' definition 'intronTable'. [funcArgNamesDifferent]
gpertea-stringtie-4b2320a/tablemaker.h:151:86: note: Function 'rc_addFeatures' argument 6 names different: declaration 'idata' definition 'intronTable'.
gpertea-stringtie-4b2320a/tablemaker.cpp:207:84: note: Function 'rc_addFeatures' argument 6 names different: declaration 'idata' definition 'intronTable'.
gpertea-stringtie-4b2320a/tablemaker.cpp:82:52: style: Parameter 'f2t' can be declared as reference to const [constParameterReference]
gpertea-stringtie-4b2320a/tablemaker.cpp:85:16: style: Variable 'tset' can be declared as reference to const [constVariableReference]
gpertea-stringtie-4b2320a/tmerge.cpp:52:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_SHIFT [valueFlowBailoutIncompleteVar]
gpertea-stringtie-4b2320a/tmerge.cpp:28:11: warning: If resource allocation fails, then there is a possible null pointer dereference: samh [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assignment 'samh=std::fopen(samhname.chars(),"w")', assigned value is 0
gpertea-stringtie-4b2320a/tmerge.cpp:28:11: note: Null pointer dereference
gpertea-stringtie-4b2320a/tmerge.cpp:38:12: warning: If resource allocation fails, then there is a possible null pointer dereference: samh [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assignment 'samh=std::fopen(samhname.chars(),"w")', assigned value is 0
gpertea-stringtie-4b2320a/tmerge.cpp:38:12: note: Null pointer dereference
gpertea-stringtie-4b2320a/tmerge.cpp:41:11: warning: If resource allocation fails, then there is a possible null pointer dereference: samh [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assignment 'samh=std::fopen(samhname.chars(),"w")', assigned value is 0
gpertea-stringtie-4b2320a/tmerge.cpp:41:11: note: Null pointer dereference
gpertea-stringtie-4b2320a/tmerge.cpp:42:10: warning: If resource allocation fails, then there is a possible null pointer dereference: samh [nullPointerOutOfResources]
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assuming allocation function fails
gpertea-stringtie-4b2320a/tmerge.cpp:26:19: note: Assignment 'samh=std::fopen(samhname.chars(),"w")', assigned value is 0
gpertea-stringtie-4b2320a/tmerge.cpp:42:10: note: Null pointer dereference
gpertea-stringtie-4b2320a/tmerge.cpp:15:17: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/tmerge.cpp:15:44: style: C-style pointer casting [cstyleCast]
gpertea-stringtie-4b2320a/gclib/GBase.h:253:6: error: Null pointer dereference: ptr [ctunullpointer]
gpertea-stringtie-4b2320a/gclib/GBase.h:291:9: note: Assignment 'tmp=NULL', assigned value is 0
gpertea-stringtie-4b2320a/gclib/GBase.h:292:14: note: Calling function GMalloc, 1st argument is null
gpertea-stringtie-4b2320a/gclib/GBase.h:253:6: note: Dereferencing argument ptr that is null
diff:
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:111:14: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:111:14: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:115:14: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:115:14: style: Either there is a missing 'override', or the member function 'GHashSet::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:119:6: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:119:6: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:217:13: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:229:4: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:241:4: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:252:3: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Clear' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:289:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Find' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:306:10: style:inconclusive: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::operator[]' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , CNonExon * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GFastaRec * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GPVec < GffObj > * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GeneCDSChain * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , GffNameInfo * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:320:14: style: Either there is a missing 'override', or the member function 'GHashMap < const char * , int , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::hasKey' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:80:17: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Add' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:80:17: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Add' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:88:17: style: Either there is a missing 'override', or the member function 'GHashSet < const char * , GHashKey_wyHash < const char * > , GHashKey_Eq < const char * > , uint64_t >::Remove' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/GHashMap.hh:88:17: style:inconclusive: Either there is a missing 'override', or the member function 'GHashSet::Remove' can be const. [functionConst]
head gpertea-stringtie-4b2320a/gclib/GSam.h:184:14: style: The member function 'GSamRecord::bam_update' can be static. [functionStatic]
head gpertea-stringtie-4b2320a/gclib/gff.h:502:6: style: Either there is a missing 'override', or the member function 'GffNameList::removeName' can be static. [functionStatic]


DONE